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I know you need It for a Secret Mission at some point late In the game but It wasnt untill after I watched Kaddy gamer's walkthrough on youtube (aka KADFC on Gamefaqs) that, from what the video had shown, you get It from backtracking to Mantiac after finding the small Oasis to refill your cantinas, sleep at the Inn and watch a cutscene.
I'm at Mt. Tezma after reuniting with Judith, Is It still possible to get Mother's Memento?
http://www.youtube.com/watch?v=vFldBVWFgWo WARNING: This link WILL give you a nice boot mark on your head!
usual things people will miss are Rita, Estelle, and Judith's best non-fell arm weapons, which are not attainable even after you create a save after beating the boss
accessory wise, probably the karona symbol (cow quest)
Title wise, the ones that matter, people will miss Karol's giganto quest, and Yuri's dark enforcer title
also, unless you're bent on doing all the Secret Missions, I'd recommend waiting for a second playthrough if you're doing it because of the 'extra drops when you complete a SM', don't bother from what I'm seeing so far, none of the items are exclusive or unique to those bosses that they otherwise wouldn't have dropped normally
I think some bosses do indeed drop items they wouldn't drop otherwise due to Secret Mission. For example, after accidentally killing Schwann about 8 times trying to get his Secret Mission (with my weakest weapons equipped too >_>) I got an Imperial Prestige when I did successfully complete the mission instead of just a force ring. I only noticed it in this particular instance, so I'm not sure of the Secret Missions unlock items that are "OMG must have!". I've managed to get all the Secret Missions except the second one in this play through (b/c I didn't know they existed, lol), so maybe during my second one I will post if I note any items that I consider must-haves.
I suspect some/most of them can be obtained during the game at a later point.